X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=d5ddd1bbceb5f055ccc48157be84603ea09a4720;hb=371f4bc519ea38c78f1c6f003df82769c130ac2e;hp=4be63e44850cfde4040b7217bfabf3ba13d16171;hpb=6bfaf3d3a82e4eece77dc1c2d83aede7c4dbb690;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 4be63e4..d5ddd1b 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -21,11 +21,9 @@ package jalview.gui;
 import MCview.*;
 
 import jalview.analysis.*;
-
 import jalview.datamodel.*;
-
-
 import jalview.schemes.*;
+import jalview.commands.ChangeCaseCommand;
 
 import java.awt.*;
 import java.awt.event.*;
@@ -82,6 +80,9 @@ public class PopupMenu extends JPopupMenu
   JMenuItem enterPDB = new JMenuItem();
   JMenuItem discoverPDB = new JMenuItem();
   JMenu outputMenu = new JMenu();
+  JMenuItem sequenceFeature = new JMenuItem();
+  JMenuItem textColour = new JMenuItem();
+  JMenu jMenu1 = new JMenu();
 
   /**
      * Creates a new PopupMenu object.
@@ -143,8 +144,7 @@ public class PopupMenu extends JPopupMenu
 
         if (seq != null)
         {
-          int start = Math.max(sequence.getName().length()-15, 0);
-          sequenceMenu.setText(sequence.getName().substring(start));
+          sequenceMenu.setText(sequence.getName());
 
           JMenuItem menuItem;
           if( seq.getDatasetSequence().getPDBId() != null)
@@ -180,7 +180,7 @@ public class PopupMenu extends JPopupMenu
           add(menuItem);
 
           if(ap.av.getSelectionGroup() !=null
-             && ap.av.getSelectionGroup().getSize(false)>1)
+             && ap.av.getSelectionGroup().getSize()>1)
           {
             menuItem = new JMenuItem("Represent Group with " + seq.getName());
             menuItem.addActionListener(new java.awt.event.ActionListener()
@@ -372,7 +372,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    groupName_actionPerformed(e);
+                    groupName_actionPerformed();
                 }
             });
         sequenceMenu.setText("Sequence");
@@ -381,7 +381,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    sequenceName_actionPerformed(e);
+                    sequenceName_actionPerformed();
                 }
             });
         PIDColour.setFocusPainted(false);
@@ -390,7 +390,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    unGroupMenuItem_actionPerformed(e);
+                    unGroupMenuItem_actionPerformed();
                 }
             });
 
@@ -399,7 +399,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    outline_actionPerformed(e);
+                    outline_actionPerformed();
                 }
             });
         nucleotideMenuItem.setText("Nucleotide");
@@ -407,7 +407,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    nucleotideMenuItem_actionPerformed(e);
+                    nucleotideMenuItem_actionPerformed();
                 }
             });
         colourMenu.setText("Group Colour");
@@ -417,7 +417,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    showBoxes_actionPerformed(e);
+                    showBoxes_actionPerformed();
                 }
             });
         showText.setText("Text");
@@ -426,7 +426,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    showText_actionPerformed(e);
+                    showText_actionPerformed();
                 }
             });
         showColourText.setText("Colour Text");
@@ -434,7 +434,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    showColourText_actionPerformed(e);
+                    showColourText_actionPerformed();
                 }
             });
     editMenu.setText("Edit");
@@ -443,7 +443,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        cut_actionPerformed(e);
+        cut_actionPerformed();
       }
     });
     upperCase.setText("To Upper Case");
@@ -451,7 +451,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        upperCase_actionPerformed(e);
+        changeCase(e);
       }
     });
     copy.setText("Copy");
@@ -459,7 +459,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        copy_actionPerformed(e);
+        copy_actionPerformed();
       }
     });
     lowerCase.setText("To Lower Case");
@@ -467,7 +467,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        lowerCase_actionPerformed(e);
+        changeCase(e);
       }
     });
     toggle.setText("Toggle Case");
@@ -475,7 +475,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        toggle_actionPerformed(e);
+        changeCase(e);
       }
     });
     pdbMenu.setText("Associate Structure with Sequence");
@@ -484,7 +484,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        pdbFromFile_actionPerformed(e);
+        pdbFromFile_actionPerformed();
       }
     });
     enterPDB.setText("Enter PDB Id");
@@ -492,7 +492,7 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        enterPDB_actionPerformed(e);
+        enterPDB_actionPerformed();
       }
     });
     discoverPDB.setText("Discover PDB ids");
@@ -500,25 +500,37 @@ public class PopupMenu extends JPopupMenu
     {
       public void actionPerformed(ActionEvent e)
       {
-        discoverPDB_actionPerformed(e);
+        discoverPDB_actionPerformed();
       }
     });
     outputMenu.setText("Output to Textbox...");
+    sequenceFeature.setText("Create Sequence Feature");
+    sequenceFeature.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sequenceFeature_actionPerformed();
+      }
+    });
+    textColour.setText("Text Colour");
+    textColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        textColour_actionPerformed();
+      }
+    });
+    jMenu1.setText("Group");
     add(groupMenu);
 
     add(sequenceMenu);
     groupMenu.add(editMenu);
     groupMenu.add(outputMenu);
-    groupMenu.addSeparator();
-    groupMenu.add(groupName);
-    groupMenu.add(unGroupMenuItem);
-        groupMenu.add(colourMenu);
-    groupMenu.add(showBoxes);
-        groupMenu.add(showText);
-        groupMenu.add(showColourText);
-    groupMenu.add(outline);
-        sequenceMenu.add(sequenceName);
+    groupMenu.add(sequenceFeature);
+    groupMenu.add(jMenu1);
+    sequenceMenu.add(sequenceName);
     sequenceMenu.add(pdbMenu);
+    colourMenu.add(textColour);
     colourMenu.add(noColourmenuItem);
         colourMenu.add(clustalColour);
         colourMenu.add(BLOSUM62Colour);
@@ -565,12 +577,19 @@ public class PopupMenu extends JPopupMenu
     pdbMenu.add(pdbFromFile);
     pdbMenu.add(enterPDB);
     pdbMenu.add(discoverPDB);
+    jMenu1.add(groupName);
+    jMenu1.add(unGroupMenuItem);
+    jMenu1.add(colourMenu);
+    jMenu1.add(showBoxes);
+    jMenu1.add(showText);
+    jMenu1.add(showColourText);
+    jMenu1.add(outline);
     noColourmenuItem.setText("None");
         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    noColourmenuItem_actionPerformed(e);
+                    noColourmenuItem_actionPerformed();
                 }
             });
 
@@ -579,7 +598,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    clustalColour_actionPerformed(e);
+                    clustalColour_actionPerformed();
                 }
             });
         zappoColour.setText("Zappo");
@@ -587,7 +606,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    zappoColour_actionPerformed(e);
+                    zappoColour_actionPerformed();
                 }
             });
         taylorColour.setText("Taylor");
@@ -595,7 +614,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    taylorColour_actionPerformed(e);
+                    taylorColour_actionPerformed();
                 }
             });
         hydrophobicityColour.setText("Hydrophobicity");
@@ -603,7 +622,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    hydrophobicityColour_actionPerformed(e);
+                    hydrophobicityColour_actionPerformed();
                 }
             });
         helixColour.setText("Helix propensity");
@@ -611,7 +630,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    helixColour_actionPerformed(e);
+                    helixColour_actionPerformed();
                 }
             });
         strandColour.setText("Strand propensity");
@@ -619,7 +638,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    strandColour_actionPerformed(e);
+                    strandColour_actionPerformed();
                 }
             });
         turnColour.setText("Turn propensity");
@@ -627,7 +646,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    turnColour_actionPerformed(e);
+                    turnColour_actionPerformed();
                 }
             });
         buriedColour.setText("Buried Index");
@@ -635,7 +654,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    buriedColour_actionPerformed(e);
+                    buriedColour_actionPerformed();
                 }
             });
         abovePIDColour.setText("Above % Identity");
@@ -643,7 +662,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    abovePIDColour_actionPerformed(e);
+                    abovePIDColour_actionPerformed();
                 }
             });
         userDefinedColour.setText("User Defined...");
@@ -659,7 +678,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    PIDColour_actionPerformed(e);
+                    PIDColour_actionPerformed();
                 }
             });
         BLOSUM62Colour.setText("BLOSUM62");
@@ -667,7 +686,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    BLOSUM62Colour_actionPerformed(e);
+                    BLOSUM62Colour_actionPerformed();
                 }
             });
         conservationMenuItem.setText("Conservation");
@@ -675,7 +694,7 @@ public class PopupMenu extends JPopupMenu
             {
                 public void actionPerformed(ActionEvent e)
                 {
-                    conservationMenuItem_actionPerformed(e);
+                    conservationMenuItem_actionPerformed();
                 }
             });
     }
@@ -688,7 +707,7 @@ public class PopupMenu extends JPopupMenu
         if (ap.overviewPanel != null)
           ap.overviewPanel.updateOverviewImage();
 
-        ap.seqPanel.repaint();
+        PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
     }
 
     /**
@@ -696,10 +715,10 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    protected void clustalColour_actionPerformed(ActionEvent e)
+    protected void clustalColour_actionPerformed()
     {
         SequenceGroup sg = getGroup();
-        sg.cs = new ClustalxColourScheme(sg.getSequences(true),
+        sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
                 ap.av.alignment.getWidth());
         refresh();
     }
@@ -709,7 +728,7 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    protected void zappoColour_actionPerformed(ActionEvent e)
+    protected void zappoColour_actionPerformed()
     {
         getGroup().cs = new ZappoColourScheme();
         refresh();
@@ -720,7 +739,7 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    protected void taylorColour_actionPerformed(ActionEvent e)
+    protected void taylorColour_actionPerformed()
     {
         getGroup().cs = new TaylorColourScheme();
         refresh();
@@ -731,7 +750,7 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+    protected void hydrophobicityColour_actionPerformed()
     {
         getGroup().cs = new HydrophobicColourScheme();
         refresh();
@@ -742,7 +761,7 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    protected void helixColour_actionPerformed(ActionEvent e)
+    protected void helixColour_actionPerformed()
     {
         getGroup().cs = new HelixColourScheme();
         refresh();
@@ -753,7 +772,7 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    protected void strandColour_actionPerformed(ActionEvent e)
+    protected void strandColour_actionPerformed()
     {
         getGroup().cs = new StrandColourScheme();
         refresh();
@@ -764,7 +783,7 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    protected void turnColour_actionPerformed(ActionEvent e)
+    protected void turnColour_actionPerformed()
     {
         getGroup().cs = new TurnColourScheme();
         refresh();
@@ -775,7 +794,7 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    protected void buriedColour_actionPerformed(ActionEvent e)
+    protected void buriedColour_actionPerformed()
     {
         getGroup().cs = new BuriedColourScheme();
         refresh();
@@ -786,7 +805,7 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    public void nucleotideMenuItem_actionPerformed(ActionEvent e)
+    public void nucleotideMenuItem_actionPerformed()
     {
         getGroup().cs = new NucleotideColourScheme();
         refresh();
@@ -797,7 +816,7 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    protected void abovePIDColour_actionPerformed(ActionEvent e)
+    protected void abovePIDColour_actionPerformed()
     {
         SequenceGroup sg = getGroup();
         if(sg.cs==null)
@@ -805,9 +824,9 @@ public class PopupMenu extends JPopupMenu
 
         if (abovePIDColour.isSelected())
         {
-            sg.cs.setConsensus(AAFrequency.calculate(
-                    sg.getSequences(true), 0,
-                    ap.av.alignment.getWidth()));
+          sg.cs.setConsensus(AAFrequency.calculate(
+              sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+              sg.getEndRes() + 1));
 
             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
                     getGroup().getName());
@@ -842,18 +861,20 @@ public class PopupMenu extends JPopupMenu
 
          sg.cs = udc;
        }
+       refresh();
      }
     /**
      * DOCUMENT ME!
      *
      * @param e DOCUMENT ME!
      */
-    protected void PIDColour_actionPerformed(ActionEvent e)
+    protected void PIDColour_actionPerformed()
     {
         SequenceGroup sg = getGroup();
         sg.cs = new PIDColourScheme();
-        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
-                ap.av.alignment.getWidth()));
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences),
+                                                 sg.getStartRes(),
+                                                 sg.getEndRes() + 1));
         refresh();
     }
 
@@ -862,14 +883,15 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+    protected void BLOSUM62Colour_actionPerformed()
     {
         SequenceGroup sg = getGroup();
 
         sg.cs = new Blosum62ColourScheme();
 
-        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
-                ap.av.alignment.getWidth()));
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences),
+                                                 sg.getStartRes(),
+                                                 sg.getEndRes() + 1));
 
         refresh();
     }
@@ -879,7 +901,7 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    protected void noColourmenuItem_actionPerformed(ActionEvent e)
+    protected void noColourmenuItem_actionPerformed()
     {
         getGroup().cs = null;
         refresh();
@@ -890,7 +912,7 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    protected void conservationMenuItem_actionPerformed(ActionEvent e)
+    protected void conservationMenuItem_actionPerformed()
     {
         SequenceGroup sg = getGroup();
         if(sg.cs==null)
@@ -900,8 +922,9 @@ public class PopupMenu extends JPopupMenu
         {
             Conservation c = new Conservation("Group",
                     ResidueProperties.propHash, 3,
-                    sg.getSequences(true), 0,
-                    ap.av.alignment.getWidth());
+                    sg.getSequences(ap.av.hiddenRepSequences),
+                    sg.getStartRes(),
+                    sg.getEndRes() + 1);
 
             c.calculate();
             c.verdict(false, ap.av.ConsPercGaps);
@@ -924,48 +947,26 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    protected void groupName_actionPerformed(ActionEvent e)
-    {
-        SequenceGroup sg = getGroup();
-        String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
-                "Enter new group name", "Edit group name",
-                JOptionPane.QUESTION_MESSAGE);
-
-        if (reply == null)
-        {
-            return;
-        }
-
-        sg.setName(reply);
-        groupName.setText(reply);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void analyze_actionPerformed(ActionEvent e)
+    protected void groupName_actionPerformed()
     {
-        CutAndPasteTransfer cap = new CutAndPasteTransfer();
-        JInternalFrame frame = new JInternalFrame();
-        frame.setContentPane(cap);
-        Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
 
-        SequenceGroup sg = getGroup();
-        StringBuffer sb = new StringBuffer();
+      SequenceGroup sg = getGroup();
+      EditNameDialog dialog = new EditNameDialog(sg.getName(),
+                                                 sg.getDescription(),
+                                                 "       Group Name ",
+                                                 "Group Description ",
+                                                 "Edit Group Name/Description");
 
-        for (int i = 0; i < sg.getSize(false); i++)
-        {
-            Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);
-            sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
-            sb.append("\n");
-        }
+      if (!dialog.accept)
+      {
+        return;
+      }
 
-        sb.append("Something amazing will happen soon");
-        cap.setText(sb.toString());
+      sg.setName(dialog.getName());
+      sg.setDescription(dialog.getDescription());
     }
 
+
     /**
      * DOCUMENT ME!
      *
@@ -986,40 +987,22 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    void sequenceName_actionPerformed(ActionEvent e)
+    void sequenceName_actionPerformed()
     {
-      JLabel idlabel = new JLabel(  "       Sequence Name ");
-      JLabel desclabel = new JLabel("Sequence Description ");
-      idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
-      desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
-      JTextField id = new JTextField(sequence.getName(), 40);
-      JTextField description = new JTextField(sequence.getDescription(), 40);
-      JPanel panel = new JPanel(new BorderLayout());
-      JPanel panel2 = new JPanel(new BorderLayout());
-      panel2.add(idlabel, BorderLayout.WEST);
-      panel2.add(id, BorderLayout.CENTER);
-      panel.add(panel2, BorderLayout.NORTH);
-      panel2 = new JPanel(new BorderLayout());
-      panel2.add(desclabel, BorderLayout.WEST);
-      panel2.add(description, BorderLayout.CENTER);
-      panel.add(panel2, BorderLayout.SOUTH);
-
-
-       int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
-          panel, "Edit Sequence Name/Description",
-          JOptionPane.OK_CANCEL_OPTION );
-
-
-        if (reply != JOptionPane.OK_OPTION )
+      EditNameDialog dialog = new EditNameDialog(sequence.getName(),
+                                                 sequence.getDescription(),
+                                                 "       Sequence Name ",
+                                                 "Sequence Description ",
+                                                 "Edit Sequence Name/Description");
+
+        if (!dialog.accept)
         {
             return;
         }
 
-        String s = id.getText();
-
-        if (s != null)
+        if (dialog.getName() != null)
         {
-            if (s.indexOf(" ") > -1)
+            if (dialog.getName().indexOf(" ") > -1)
             {
                 JOptionPane.showMessageDialog(ap,
                     "Spaces have been converted to \"_\"",
@@ -1027,14 +1010,15 @@ public class PopupMenu extends JPopupMenu
                     JOptionPane.WARNING_MESSAGE);
             }
 
-            s = s.replace(' ', '_');
-            sequence.getDatasetSequence().setName(s);
-            sequence.setName(s);
+            sequence.setName(dialog.getName().replace(' ', '_'));
             ap.repaint();
         }
 
-        sequence.getDatasetSequence().setDescription(description.getText());
-        sequence.setDescription(description.getText());
+        sequence.setDescription(dialog.getDescription());
+
+        ap.av.firePropertyChange("alignment", null,
+                                  ap.av.getAlignment().getSequences());
+
     }
 
     /**
@@ -1042,7 +1026,7 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    void unGroupMenuItem_actionPerformed(ActionEvent e)
+    void unGroupMenuItem_actionPerformed()
     {
         SequenceGroup sg = ap.av.getSelectionGroup();
         ap.av.alignment.deleteGroup(sg);
@@ -1056,7 +1040,7 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    protected void outline_actionPerformed(ActionEvent e)
+    protected void outline_actionPerformed()
     {
         SequenceGroup sg = getGroup();
         Color col = JColorChooser.showDialog(this, "Select Outline Colour",
@@ -1075,7 +1059,7 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    public void showBoxes_actionPerformed(ActionEvent e)
+    public void showBoxes_actionPerformed()
     {
         getGroup().setDisplayBoxes(showBoxes.isSelected());
         refresh();
@@ -1086,7 +1070,7 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    public void showText_actionPerformed(ActionEvent e)
+    public void showText_actionPerformed()
     {
         getGroup().setDisplayText(showText.isSelected());
         refresh();
@@ -1097,7 +1081,7 @@ public class PopupMenu extends JPopupMenu
      *
      * @param e DOCUMENT ME!
      */
-    public void showColourText_actionPerformed(ActionEvent e)
+    public void showColourText_actionPerformed()
     {
         getGroup().setColourText(showColourText.isSelected());
         refresh();
@@ -1124,86 +1108,124 @@ public class PopupMenu extends JPopupMenu
     void hideSequences(boolean representGroup)
     {
       SequenceGroup sg = ap.av.getSelectionGroup();
-      if(sg==null || sg.getSize(false)<1)
+      if(sg==null || sg.getSize()<1)
       {
-        ap.av.hideSequence(sequence);
+        ap.av.hideSequence(new SequenceI[]{sequence});
         return;
       }
 
-        int index = 0;
-        while(index < sg.getSize(false))
-        {
-          if(representGroup && sg.getSequenceAt(index)!=sequence)
-          {
-            sequence.addHiddenSequence(sg.getSequenceAt(index));
-            ap.av.hideSequence(sg.getSequenceAt(index));
-          }
-          else if(!representGroup)
-          {
-            ap.av.hideSequence(sg.getSequenceAt(index));
-          }
-          index ++;
-        }
+      ap.av.setSelectionGroup(null);
 
-        ap.av.setSelectionGroup(null);
+      if (representGroup)
+      {
+        ap.av.hideRepSequences(sequence, sg);
+
+        return;
+      }
+
+      int gsize = sg.getSize();
+      SequenceI[] hseqs;
+
+      hseqs = new SequenceI[gsize];
+
+      int index = 0;
+      for (int i = 0; i < gsize; i++)
+      {
+        hseqs[index++] = sg.getSequenceAt(i);
+      }
+
+      ap.av.hideSequence(hseqs);
     }
 
-  public void copy_actionPerformed(ActionEvent e)
+  public void copy_actionPerformed()
   {
     ap.alignFrame.copy_actionPerformed(null);
   }
 
-  public void cut_actionPerformed(ActionEvent e)
+  public void cut_actionPerformed()
   {
     ap.alignFrame.cut_actionPerformed(null);
   }
 
-  public void upperCase_actionPerformed(ActionEvent e)
+  void changeCase(ActionEvent e)
   {
+    Object source = e.getSource();
     SequenceGroup sg = ap.av.getSelectionGroup();
-    if(sg==null)
-      return;
-
-    for(int g=0; g<sg.getSize(true); g++)
+    Vector regions = new Vector();
+    if (sg != null)
     {
-    ( (SequenceI)sg.getSequences(true).elementAt(g))
-        .changeCase(true, sg.getStartRes(), sg.getEndRes()+1);
-    }
-    ap.repaint();
-  }
+      int start = sg.getStartRes();
+      int end = sg.getEndRes() + 1;
 
-  public void lowerCase_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if(sg==null)
-      return;
+      do
+      {
+        if (ap.av.hasHiddenColumns)
+        {
+          if(start==0)
+            start = ap.av.colSel.adjustForHiddenColumns(start);
+
+          end = ap.av.colSel.getHiddenBoundaryRight(start);
+          if (start == end)
+            end = sg.getEndRes() + 1;
+          if (end > sg.getEndRes())
+            end = sg.getEndRes() + 1;
+        }
 
-    for(int g=0; g<sg.getSize(true); g++)
-    {
-       ( (SequenceI)sg.getSequences(true).elementAt(g))
-           .changeCase(false, sg.getStartRes(), sg.getEndRes()+1);
-    }
-    ap.repaint();
-  }
+        regions.addElement(new int[]
+                           {start, end});
 
-  public void toggle_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if (sg == null)
-      return;
+        if (ap.av.hasHiddenColumns)
+        {
+          start = ap.av.colSel.adjustForHiddenColumns(end);
+          start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
+        }
+      }
+      while (end < sg.getEndRes());
 
-    for (int g = 0; g < sg.getSize(true); g++)
-    {
-      ( (SequenceI)sg.getSequences(true).elementAt(g))
-          .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
-    }
+      int[][] startEnd = new int[regions.size()][2];
+      for (int i = 0; i < regions.size(); i++)
+      {
+        startEnd[i] = (int[]) regions.elementAt(i);
+      }
 
-    ap.repaint();
+
+      String description;
+      int caseChange;
+
+      if(source==toggle)
+      {
+        description = "Toggle Case";
+        caseChange = ChangeCaseCommand.TOGGLE_CASE;
+      }
+      else if(source==upperCase)
+      {
+        description = "To Upper Case";
+        caseChange = ChangeCaseCommand.TO_UPPER;
+      }
+      else
+      {
+        description = "To Lower Case";
+        caseChange = ChangeCaseCommand.TO_LOWER;
+      }
+
+      ChangeCaseCommand caseCommand = new ChangeCaseCommand(
+          description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
+          startEnd, caseChange
+          );
+
+      ap.alignFrame.addHistoryItem(caseCommand);
+
+
+      ap.av.firePropertyChange("alignment", null,
+                                ap.av.getAlignment().getSequences());
+
+    }
   }
 
   public void outputText_actionPerformed(ActionEvent e)
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    cap.setForInput(null);
     Desktop.addInternalFrame(cap,
                              "Alignment output - " + e.getActionCommand(), 600,
                              500);
@@ -1223,7 +1245,7 @@ public class PopupMenu extends JPopupMenu
   }
 
 
-  public void pdbFromFile_actionPerformed(ActionEvent e)
+  public void pdbFromFile_actionPerformed()
   {
      jalview.io.JalviewFileChooser chooser
          = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
@@ -1271,7 +1293,7 @@ public class PopupMenu extends JPopupMenu
 
   }
 
-  public void enterPDB_actionPerformed(ActionEvent e)
+  public void enterPDB_actionPerformed()
   {
     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
         "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
@@ -1285,9 +1307,43 @@ public class PopupMenu extends JPopupMenu
     }
   }
 
-  public void discoverPDB_actionPerformed(ActionEvent e)
+  public void discoverPDB_actionPerformed()
   {
     new jalview.io.DBRefFetcher(
              ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
   }
+
+  public void sequenceFeature_actionPerformed()
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if(sg==null)
+      return;
+
+    int gSize= sg.getSize();
+    SequenceI [] seqs = new SequenceI[gSize];
+    SequenceFeature [] features = new SequenceFeature[gSize];
+
+    for (int i = 0; i < gSize; i++)
+    {
+      seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
+      int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
+      int end = sg.findEndRes(sg.getSequenceAt(i));
+      features[i] = new SequenceFeature(null,null, null,start,end,"Jalview");
+    }
+
+    if (ap.seqPanel.seqCanvas.getFeatureRenderer()
+        .createNewFeatures(seqs, features))
+    {
+      ap.alignFrame.showSeqFeatures.setSelected(true);
+      ap.av.setShowSequenceFeatures(true);
+      ap.highlightSearchResults(null);
+    }
+  }
+
+  public void textColour_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    if (sg != null)
+      new TextColourChooser().chooseColour(ap, sg);
+  }
 }